A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

We describe a statistical framework for reconstructing the sequence of transmission events between observed cases of an endemic infectious disease using genetic, temporal and spatial information. Previous approaches to reconstructing transmission trees have assumed all infections in the study area originated from a single introduction and that a large fraction of cases were observed. There are as yet no approaches appropriate for endemic situations in which a disease is already well established in a host population and in which there may be multiple origins of infection, or that can enumerate unobserved infections missing from the sample. Our proposed framework addresses these shortcomings, enabling reconstruction of partially observed transmission trees and estimating the number of cases missing from the sample. Analyses of simulated datasets show the method to be accurate in identifying direct transmissions, while introductions and transmissions via one or more unsampled intermediate cases could be identified at high to moderate levels of case detection. When applied to partial genome sequences of rabies virus sampled from an endemic region of South Africa, our method reveals several distinct transmission cycles with little contact between them, and direct transmission over long distances suggesting significant anthropogenic influence in the movement of infected dogs

Strongly correlated Fermions strongly coupled to light

Strong quantum correlations in matter are responsible for some of the most extraordinary properties of material, from magnetism to high-temperature superconductivity, but their integration in quantum devices requires a strong, coherent coupling with photons, which still represents a formidable technical challenge in solid state systems. In cavity quantum electrodynamics, quantum gases such as Bose-Einstein condensates or lattice gases have been strongly coupled with light. However, neither Fermionic quantum matter, comparable to electrons in solids, nor atomic systems with controlled interactions, have thus far been strongly coupled with photons. Here we report on the strong coupling of a quantum-degenerate unitary Fermi gas with light in a high finesse cavity. We map out the spectrum of the coupled system and observe well resolved dressed states, resulting from the strong coupling of cavity photons with each spin component of the gas. We investigate spin-balanced and spin-polarized gases and find quantitative agreement with ab-initio calculation describing light-matter interaction. Our system offers complete and simultaneous control of atom-atom and atom-photon interactions in the quantum degenerate regime, opening a wide range of perspectives for quantum simulation.Comment: Updated reference

Threats to the quality of marking of the national senior certificate examinations in the Northern Cape

Examinations are regarded as vital instruments not only to determine the progress and success of learners, but also the quality of an education system. Owing to these high stakes, South Africa places enormous emphasis on the National Senior Certificate examination. Although quality should be ensured by an effective, accurate and a high standard in the marking process, complaints suggest that there may be threats to the quality of marking and, by implication, to the education system itself. This exploratory study reports on the possible threats to a high standard of marking that emerged from data generated through semi-structured interviews with various role-players involved in the marking process. The findings suggest that the threats relate to the appointment of markers, the competency of the markers and an overall lack of confidence in the marking process. We conclude the article by proposing various recommendations to curb the identified threats to accurate marking

Comparison of semirigorous and empirical models derived using data quality assessment methods

With the increase in available data and the stricter control requirements for mineral processes, the development of automated methods for data processing and model creation are becoming increasingly important. In this paper, the application of data quality assessment methods for the development of semirigorous and empirical models of a primary milling circuit in a platinum concentrator plant is investigated to determine their validity and how best to handle multivariate input data. The data set used consists of both routine operating data and planned step tests. Applying the data quality assessment method to this data set, it was seen that selecting the appropriate subset of variables for multivariate assessment was difficult. However, it was shown that it was possible to identify regions of sufficient value for modeling. Using the identified data, it was possible to fit empirical linear models and a semirigorous nonlinear model. As expected, models obtained from the routine operating data were, in general, worse than those obtained from the planned step tests. However, using the models obtained from routine operating data as the initial seed models for the automated advanced process control methods would be extremely helpful. Therefore, it can be concluded that the data quality assessment method was able to extract and identify regions sufficient and acceptable for modeling

Experimental evidence for melt partitioning between olivine and orthopyroxene in partially molten harzburgite

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Solid Earth 121 (2016): 5776–5793, doi:10.1002/2016JB013122.Observations of dunite channels in ophiolites and uranium series disequilibria in mid-ocean ridge basalt suggest that melt transport in the upper mantle beneath mid-ocean ridges is strongly channelized. We present experimental evidence that spatial variations in mineralogy can also focus melt on the grain scale. This lithologic melt partitioning, which results from differences in the interfacial energies associated with olivine-melt and orthopyroxene-melt boundaries, may complement other melt focusing mechanisms in the upper mantle such as mechanical shear and pyroxene dissolution. We document here lithologic melt partitioning in olivine-/orthopyroxene-basaltic melt samples containing nominal olivine to orthopyroxene ratio of 3 to 2 and melt fractions of 0.02 to 0.20. Experimental samples were imaged using synchrotron-based X-ray microcomputed tomography at a resolution of 700 nm per voxel. By analyzing the local melt fraction distributions associated with olivine and orthopyroxene grains in each sample, we found that the melt partitioning coefficient, i.e., the ratio of melt fraction around olivine to that around orthopyroxene grains, varies between 1.1 and 1.6. The permeability and electrical conductivity of our digital samples were estimated using numerical models and compared to those of samples containing only olivine and basaltic melt. Our results suggest that lithologic melt partitioning and preferential localization of melt around olivine grains might play a role in melt focusing, potentially enhancing average melt ascent velocities.National Science Foundation Grant Numbers: 1250338, 1551300; Basic Energy Sciences Grant Number: DEFG0207ER15916; Advanced Photon Source Grant Number: DE-AC02-06CH113572017-02-2

Characteristics of owned dogs in rabies endemic KwaZulu-Natal province, South Africa

BACKGROUND : Canine rabies has been enzootic in the dog population of the KwaZulu-Natal province of South Africa since the mid-1970s and has been associated with high rates of human exposures and frequent transmissions to other domestic animal species. Several decades of control efforts, consisting primarily of mass vaccination programs, have previously failed to sufficiently curb rabies in the province. Despite this history of canine rabies, the target canine population has never been extensively studied or quantified. For efficient and effective vaccination campaign planning, the target population must be evaluated and understood. This study reports evaluated observations from survey records captured through a cross sectional observational study regarding canine populations and dog owners in rabies enzootic KwaZulu-Natal province, South Africa. The objective of this study was to aid government veterinary services in their current and ongoing efforts to eliminate canine rabies in the province by gaining information about the size and distribution of the owned dog population. RESULTS : Thirty-eight percent of the households owned one or more dogs, with rural areas surveyed containing a significantly higher number of owned dogs than urban areas. The mean dog/person ratio for this study was 1:7.7 (range 1:5.4–1:31). The provincial sex ratio was 1.5:1 male to female, with the percentages for male dogs across the communities ranging from 53 to 61.5%. The age structure of this dog population indicates a high turnover rate. Dogs were kept mostly for guarding homes or livestock. Eighty-four percent of dogs had received a rabies vaccine at some point in their lifetime, almost all during a rabies campaign. CONCLUSIONS : The study indicates the majority of owned dogs can be handled by at least one member of the household, thus can be made readily accessible for rabies vaccination during a campaign. Characteristics of owned dogs in the province were similar to those studied in other African countries; however, there were remarkable differences in age, sex and husbandry practices compared to dogs in eastern or northern Africa. These geographical differences lend credence to the theory that canine populations are heterogeneous; therefore, target populations should be evaluated prior to intervention planning.The University of Pretoria, Onderstepoort and the Humane Society International.https://bmcvetres.biomedcentral.comam2019BiochemistryGeneticsMicrobiology and Plant PathologyParaclinical Science

Density-wave ordering in a unitary Fermi gas with photon-mediated interactions

A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the last decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering, pairing and superfluidity, and the crossover from a Bardeen-Cooper-Schrieffer (BCS) superfluid to a Bose-Einstein condensate (BEC). Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength DW order is stabilized in the system, which we identify via its superradiant light scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the BCS-BEC crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.Comment: 11 pages, 7 figure

Lagos bat virus, an under-reported rabies-related lyssavirus

Lagos bat virus (LBV), one of the 17 accepted viral species of the Lyssavirus genus, was the first rabies-related virus described in 1956. This virus is endemic to the African continent and is rarely encountered. There are currently four lineages, although the observed genetic diversity exceeds existing lyssavirus species demarcation criteria. Several exposures to rabid bats infected with LBV have been reported; however, no known human cases have been reported to date. This review provides the history of LBV and summarizes previous knowledge as well as new detections. Genetic diversity, pathogenesis and prevention are re-evaluated and discussed.This research is supported in part by the South African Research Chair Initiative (held by Wanda Markotter) of the Department of Science and Innovation and administered by the National Research Foundation of South Africa (UID: 98339). The National Research Foundation funded the equipment based at the DNA Sanger sequencing facility in the Faculty of Natural and Agricultural Sciences, University of Pretoria (UID: 78566).https://www.mdpi.com/journal/virusesdm2022Medical Virolog

Electrochemotherapy in radiotherapy-resistant epidural spinal cord compression in metastatic cancer patients

Objective: To report efficacy and safety of percutaneous electrochemotherapy (ECT) in patients with radiotherapy-resistant metastatic epidural spinal cord compression (MESCC). Material/ methods: This retrospective study analyzed all consecutive patients treated with bleomycin-based ECT between February-2020 and September-2022 in a single tertiary referral cancer center. Changes in pain were evaluated with the Numerical Rating Score (NRS), in neurological deficit with the Neurological Deficit Scale, and changes in epidural spinal cord compression were evaluated with the epidural spinal cord compression scale (ESCCS) using an MRI. Results: Forty consecutive solid tumour patients with previously radiated MESCC and no effective systemic treatment options were eligible. With a median follow-up of 5.1 months [1-19.1], toxicities were temporary acute radicular pain (25%), prolonged radicular hypoesthesia (10%), and paraplegia (7.5%). At 1 month, pain was significantly improved over baseline (median NRS: 1.0 [0-8] versus 7.0 [1.0-10], P < .001) and neurological benefits were considered as marked (28%), moderate (28%), stable (38%), or worse (8%). Three-month follow-up (21 patients) confirmed improved over baseline (median NRS: 2.0 [0-8] versus 6.0 [1.0-10], P < .001) and neurological benefits were considered as marked (38%), moderate (19%), stable (33.5%), and worse (9.5%). One-month post-treatment MRI (35 patients) demonstrated complete response in 46% of patients by ESCCS, partial response in 31%, stable disease in 23%, and no patients with progressive disease. Three-month post-treatment MRI (21 patients) demonstrated complete response in 28.5%, partial response in 38%, stable disease in 24%, and progressive disease in 9.5%. Conclusions: This study provides the first evidence that ECT can rescue radiotherapy-resistant MESCC